A Monte Carlo simulation study of a Janus discotic liquid crystal droplet.

The study of discotic liquid crystals (DLCs) under spherical confinement has gained considerable significance due to its relevance in the design and optimization of advanced materials with tailored properties. The unique characteristics of DLC fluids, coupled with confinement within a spherical Janus surface, offer a compelling avenue for exploring novel behaviors and emergent phenomena. In this study, Monte Carlo simulations within the NpT ensemble are employed to investigate the behavior of a DLC fluid confined by a spherical Janus surface. The Janus surface is characterized by distinct hemispheres, with one promoting homeotropic (face-on) anchoring and the other planar (edge-on) anchoring. Our analysis reveals the emergence of two topological defects: one exclusively on the edge-anchoring hemisphere and the other at the boundary of both anchorings. Each topological defect possessing a topological charge ofk= +1/2. We observe that as the temperature transitions the central region of the droplet into a nematic phase, a disclination line forms, linking the two surface defects. By investigating droplets of three different sizes, we confirm that the isotropic-nematic transition is first-order for the larger droplet studied. However, this transition becomes continuous under strong confinement conditions. In contrast, the nematic-columnar transition remains first order even for smaller systems.

Phase transitions and topological defects in discotic liquid crystal droplets with planar anchoring: a Monte Carlo simulation study.

In this work we present the results of Monte Carlo (MC) simulations at the isothermal-isobaric ensemble for a discotic liquid crystal (DLC) droplet whose surface promotes edge-on (planar) anchoring. For a given pressure, we simulate an annealing process that enables observation of phase transitions within the spherical droplet. In particular, we report a first order isotropic-nematic transition as well as a nematic-columnar transition at the center of the droplet. We found the appearance of topological defects consisting of two disclination lines with ends at the surface of the sphere. We also observed that both transitions, isotropic-nematic and nematic-columnar, occur at lower temperatures as compared to the unconfined system.

Electronic and magnetic properties of TATA-DNA sequence driven by chemical functionalization.

The TATA box is a promoter sequence able to interact directly with the components of the basal transcription initiation machinery. We investigate the changes in the electronic and magnetic properties of a TATA-DNA sequence when functionalized with different chemical groups; using the first-principles density functional theory specifically, the TATA-DNA sequences were functionalized with methyl groups (CH3 , methylation), amino groups (NH2 , amination), imine groups (NH, imination), chloroamine groups (NCl2 , chloramination), H-adatom (hydrogenation), and Cl-adatom (chlorination). The functional groups were anchored at nitrogen atoms from adenine and oxygen atoms from thymine at sites pointed as reactive regions. We demonstrated that chemical functionalization induces significant changes in charge transfer, hydrogen bond distance, and hydrogen bond energy. The hydrogenation and imination increased the hydrogen bond energy. Results also revealed that the chemical functionalization of DNA molecules exhibit a ferromagnetic ground state, reaching magnetization up to 4.665 µB and complex magnetic ordering. We further demonstrated that the functionalization could induce tautomerism (proton migration in the base pair systems). The present study provides a theoretical basis for understanding the functionalization further into DNA molecules and visualizing possible future applications.

DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.

Regulatory factor MBF1 is highly conserved between species and has been described as a cofactor and transcription factor. In plants, several reports associate MBF1 with heat stress response. Nevertheless, the specific physical processes involved in the MBF1-DNA interaction are still far from clearly understood. We thus performed extensive molecular dynamics simulations of DNA with a homology-based modethel of the MBF1 protein. Based on recent experimental data, we proposed two B-DNA sequences, analyzing their interaction with our model of the Arabidopsis MBF1c protein (AtMBF1c) at three different temperatures: 293, 300, and 320 K, maintaining a constant pressure of 1 bar. The simulations suggest that MBF1 binds directly to the DNA, supporting the idea of its role as a transcription factor. We identified two different conformations of the MBF1 protein when bound, and characterized the specific groups of amino acids involved in the formation of the DNA-MBF1 complex. These regions of amino acids are bound mostly to the minor groove of DNA by the attraction of positively charged residues and the negatively charged backbone, but subject to the compatibility of shapes, much in the sense of a lock-and-key mechanism. We found that only with a sequence rich in CTAGA motifs at 300 K does MBF1 bind to DNA in the DNA-binding domain Cro/C1-type HTH predicted. In the rest of the systems tested, we observed non-specific DNA-MBF1 interactions. This study complements findings previously reported by others on the role of CTAGA as a DNA-binding element for MBF1c at a heat stress temperature.

Effect of the anchoring strength on the phase behaviour of discotic liquid crystals under face-on confinement.

In this study we have performed molecular dynamics simulations to study a Gay-Berne discotic fluid confined in a slab geometry for a fixed confinement length. Four different anchoring strengths with a homeotropic (face-on) configuration were studied. We found that changing the anchoring strength changes the normal component of the stress tensor, which in turn changes the density of the system's bulk. This phenomenon leads to a shift in the isotropic-nematic transition temperature. We observe that the temperature regions where the nematic phase is present diminishes as the anchoring strength increases. The anchoring strength also affects the nematic-columnar coexistence temperature-region: it spans over more temperatures at higher anchoring strengths.

Influence of anchoring in the phase behaviour of discotic liquid crystals.

Molecular dynamics simulations were performed for a Gay-Berne discotic fluid confined in a slab geometry for two different anchorings: homeotropic (face-on) and planar (edge-on), and for two different confinement lengths. Our results show that the behaviour of the more confined system in the temperature region of the isotropic-nematic transition is critically influenced by the presence of the walls: the growth of the solid-liquid crystal interface spans over the entire width of the cell, and the character of the transition is changed from first order to continuous. For all the confined systems studied, we observe a higher nematic-columnar transition temperature and a smaller nematic phase region in the phase diagram, as compared with the behaviour of the infinite system.

Non-additive simple potentials for pre-programmed self-assembly.

A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts are currently concentrated in the development of the so-called "patchy" particles. Here we follow a completely different approach and introduce a very accessible model to produce a large variety of pre-programmed two-dimensional (2D) complex structures. Our model consists of a binary mixture of particles that interact through isotropic interactions that enable them to self-assemble into targeted lattices by the appropriate choice of a small number of geometrical parameters and interaction strengths. We study the system using Monte Carlo computer simulations and, despite its simplicity, we are able to self-assemble potentially useful structures such as chains, stripes, and Kagomé, twisted Kagomé, honeycomb, square, Archimedean and quasicrystalline tilings. Our model is designed in such a way that it may be implemented using discotic particles or, alternatively, using exclusively spherical particles interacting isotropically. Thus, it represents a promising strategy for bottom-up nano-fabrication.

Self-assembly of anisotropic soft particles in two dimensions.

The self-assembly of core-corona discs interacting via anisotropic potentials is investigated using Monte Carlo computer simulations. A minimal interaction potential that incorporates anisotropy in a simple way is introduced. It consists in a core-corona architecture in which the center of the core is shifted with respect to the center of the corona. Anisotropy can thus be tuned by progressively shifting the position of the core. Despite its simplicity, the system self-organizes in a rich variety of structures including stripes, triangular and rectangular lattices, cluster crystals, unusual plastic crystals, and geometrically frustrated phases. Our results indicate that the amount of anisotropy does not alter the lattice spacing and only influences the type of clustering (stripes, micelles, etc.) of the individual particles.